[2024-01-24 14:12:47,448] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,451] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,451] [INFO] DQC Reference Directory: /var/lib/cwl/stg18a9d17e-29a1-4ef2-b759-7f661892a4b0/dqc_reference
[2024-01-24 14:12:48,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,688] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,688] [INFO] Running command: gunzip -c /var/lib/cwl/stg18905c8a-121b-4ed5-a852-ed3930b3e49f/GCF_003591655.1_ASM359165v1_genomic.fna.gz | prodigal -d GCF_003591655.1_ASM359165v1_genomic.fna/cds.fna -a GCF_003591655.1_ASM359165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:03,713] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:03,714] [INFO] Task started: HMMsearch
[2024-01-24 14:13:03,714] [INFO] Running command: hmmsearch --tblout GCF_003591655.1_ASM359165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18a9d17e-29a1-4ef2-b759-7f661892a4b0/dqc_reference/reference_markers.hmm GCF_003591655.1_ASM359165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:04,003] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:04,004] [INFO] Found 6/6 markers.
[2024-01-24 14:13:04,050] [INFO] Query marker FASTA was written to GCF_003591655.1_ASM359165v1_genomic.fna/markers.fasta
[2024-01-24 14:13:04,050] [INFO] Task started: Blastn
[2024-01-24 14:13:04,050] [INFO] Running command: blastn -query GCF_003591655.1_ASM359165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18a9d17e-29a1-4ef2-b759-7f661892a4b0/dqc_reference/reference_markers.fasta -out GCF_003591655.1_ASM359165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:04,916] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:04,920] [INFO] Selected 13 target genomes.
[2024-01-24 14:13:04,920] [INFO] Target genome list was writen to GCF_003591655.1_ASM359165v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:04,925] [INFO] Task started: fastANI
[2024-01-24 14:13:04,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg18905c8a-121b-4ed5-a852-ed3930b3e49f/GCF_003591655.1_ASM359165v1_genomic.fna.gz --refList GCF_003591655.1_ASM359165v1_genomic.fna/target_genomes.txt --output GCF_003591655.1_ASM359165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:17,404] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:17,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18a9d17e-29a1-4ef2-b759-7f661892a4b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:17,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18a9d17e-29a1-4ef2-b759-7f661892a4b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:17,417] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:17,417] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:17,417] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	100.0	1633	1638	95	conclusive
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	89.3976	896	1638	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	85.3566	1003	1638	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	84.364	887	1638	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	83.9888	906	1638	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	83.0955	887	1638	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	82.2186	705	1638	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	82.1327	720	1638	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	82.0833	708	1638	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	79.1869	503	1638	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.6181	352	1638	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.3744	284	1638	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.348	346	1638	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:17,418] [INFO] DFAST Taxonomy check result was written to GCF_003591655.1_ASM359165v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:17,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:17,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:17,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18a9d17e-29a1-4ef2-b759-7f661892a4b0/dqc_reference/checkm_data
[2024-01-24 14:13:17,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:17,471] [INFO] Task started: CheckM
[2024-01-24 14:13:17,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003591655.1_ASM359165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003591655.1_ASM359165v1_genomic.fna/checkm_input GCF_003591655.1_ASM359165v1_genomic.fna/checkm_result
[2024-01-24 14:14:02,996] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:02,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:03,017] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:03,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:03,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003591655.1_ASM359165v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:03,018] [INFO] Task started: Blastn
[2024-01-24 14:14:03,018] [INFO] Running command: blastn -query GCF_003591655.1_ASM359165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18a9d17e-29a1-4ef2-b759-7f661892a4b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003591655.1_ASM359165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:04,728] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:04,732] [INFO] Selected 7 target genomes.
[2024-01-24 14:14:04,732] [INFO] Target genome list was writen to GCF_003591655.1_ASM359165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:04,738] [INFO] Task started: fastANI
[2024-01-24 14:14:04,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg18905c8a-121b-4ed5-a852-ed3930b3e49f/GCF_003591655.1_ASM359165v1_genomic.fna.gz --refList GCF_003591655.1_ASM359165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003591655.1_ASM359165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:13,432] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:13,442] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:13,442] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003591655.1	s__Sphingobium sp003591655	100.0	1633	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016463275.1	s__Sphingobium sp016463275	93.3185	712	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019097845.1	s__Sphingobium sp019097845	92.8261	1095	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382885.1	s__Sphingobium japonicum_C	90.4296	890	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367345.1	s__Sphingobium xenophagum	89.3976	896	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.29	96.67	0.79	0.71	22	-
GCF_014280435.1	s__Sphingobium sp014280435	86.2214	978	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152865.1	s__Sphingobium cupriresistens	84.3543	888	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	98.49	0.81	0.81	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:13,445] [INFO] GTDB search result was written to GCF_003591655.1_ASM359165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:13,445] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:13,448] [INFO] DFAST_QC result json was written to GCF_003591655.1_ASM359165v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:13,448] [INFO] DFAST_QC completed!
[2024-01-24 14:14:13,448] [INFO] Total running time: 0h1m26s